Package picard.sam.SamErrorMetric
Class ReadBaseStratification
- java.lang.Object
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- picard.sam.SamErrorMetric.ReadBaseStratification
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public class ReadBaseStratification extends Object
Classes, methods, and enums that deal with the stratification of read bases and reference information.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
ReadBaseStratification.BinnedReadCycleStratifier
Stratifies into quintiles of read cycle.static class
ReadBaseStratification.CigarOperatorsInReadStratifier
Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.static class
ReadBaseStratification.CollectionStratifier
A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.static class
ReadBaseStratification.Consensus
Types of consensus reads as determined by the number of duplicates used from first and second strands.static class
ReadBaseStratification.ConsensusStratifier
Stratify by tags used during duplex and single index consensus calling.static class
ReadBaseStratification.CycleBin
An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintilesstatic class
ReadBaseStratification.FlowCellTileStratifier
Stratifies base into their read's tile which is parsed from the read-name.static class
ReadBaseStratification.FlowCellXStratifier
Stratifies base into their read's X coordinate which is parsed from the read-name.static class
ReadBaseStratification.FlowCellYStratifier
Stratifies base into their read's Y coordinate which is parsed from the read-name.static class
ReadBaseStratification.GCContentStratifier
A stratifier that uses GC (of the read) to stratify.static class
ReadBaseStratification.IndelLengthStratifier
Stratifies according to the length of an insertion or deletion.static class
ReadBaseStratification.IndelsInReadStratifier
Stratifies according to the number of indel bases (from CIGAR string) that the read has.static class
ReadBaseStratification.LongShortHomopolymer
static class
ReadBaseStratification.LongShortHomopolymerStratifier
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).static class
ReadBaseStratification.MismatchesInReadStratifier
Stratifies according to the overall mismatches (fromSAMTag.NM
) that the read has against the reference, NOT including the current base.static class
ReadBaseStratification.NsInReadStratifier
Stratify by the number of Ns found in the read.static class
ReadBaseStratification.PairOrientation
An enum for holding a reads read-pair's Orientation (i.e.static class
ReadBaseStratification.PairStratifier<T extends Comparable<T>,R extends Comparable<R>>
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.static class
ReadBaseStratification.ProperPaired
An enum to hold information about the "properness" of a read pairstatic class
ReadBaseStratification.ReadDirection
An enum for holding the direction for a read (positive strand or negative strandstatic class
ReadBaseStratification.ReadOrdinality
An enum to hold the ordinality of a readstatic interface
ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>>
The main interface for a stratifier.
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Field Summary
Fields Modifier and Type Field Description static ReadBaseStratification.RecordAndOffsetStratifier<Integer>
baseCycleStratifier
Get the one-based cycle number of the base, taking the direction of the read into accountstatic ReadBaseStratification.RecordAndOffsetStratifier<Byte>
baseQualityStratifier
Stratifies into the base-quality of the base under considerationstatic htsjdk.samtools.util.Lazy<ReadBaseStratification.PairStratifier<ReadBaseStratification.LongShortHomopolymer,Pair<Character,Character>>>
binnedHomopolymerStratifier
Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came.static ReadBaseStratification.BinnedReadCycleStratifier
binnedReadCycleStratifier
Stratifies into quintiles of read cycle.static ReadBaseStratification.ConsensusStratifier
consensusStratifier
Stratify by tags used during duplex and single index consensus calling.static ReadBaseStratification.RecordAndOffsetStratifier<Character>
currentReadBaseStratifier
Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.static ReadBaseStratification.CigarOperatorsInReadStratifier
deletionsInReadStratifier
Stratify by Deletions in the read cigars.static ReadBaseStratification.FlowCellTileStratifier
flowCellTileStratifier
Stratifies base into their read's tile which is parsed from the read-name.static ReadBaseStratification.FlowCellXStratifier
flowCellXStratifier
Stratifies base into their read's tile which is parsed from the read-name.static ReadBaseStratification.FlowCellYStratifier
flowCellYStratifier
Stratifies base into their read's tile which is parsed from the read-name.static ReadBaseStratification.GCContentStratifier
gcContentStratifier
A stratifier that uses GC (of the read) to stratify.static ReadBaseStratification.RecordAndOffsetStratifier<Integer>
homoPolymerLengthStratifier
Stratifies a base onto the length of the homopolymer preceding it (in the read direction).static ReadBaseStratification.PairStratifier<Integer,Pair<Character,Character>>
homopolymerStratifier
Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came.static ReadBaseStratification.IndelLengthStratifier
indelLengthStratifier
Stratifies into the number of bases in an insertionstatic ReadBaseStratification.IndelsInReadStratifier
indelsInReadStratifier
Stratify by Indels in the read cigars.static ReadBaseStratification.CigarOperatorsInReadStratifier
insertionsInReadStratifier
Stratify by Insertions in the read cigars.static ReadBaseStratification.RecordAndOffsetStratifier<Integer>
insertLengthStratifier
Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the readstatic ReadBaseStratification.RecordAndOffsetStratifier<Integer>
mappingQualityStratifier
Stratifies into the mapping-quality of the read under considerationstatic ReadBaseStratification.MismatchesInReadStratifier
mismatchesInReadStratifier
Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.static ReadBaseStratification.RecordAndOffsetStratifier<Character>
nextReadBaseStratifier
Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e.static picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<String>
nonStratifier
A constant stratifier which places all the reads into a single stratum.static int
NOT_ALIGNED_ERROR
static ReadBaseStratification.NsInReadStratifier
nsInReadStratifier
Stratify by the number of Ns found in the read.static ReadBaseStratification.RecordAndOffsetStratifier<String>
oneBasePaddedContextStratifier
Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencerstatic ReadBaseStratification.PairStratifier<Character,Character>
postDiNucleotideStratifier
Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.static ReadBaseStratification.PairStratifier<Character,Character>
preDiNucleotideStratifier
Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.static ReadBaseStratification.RecordAndOffsetStratifier<Character>
previousReadBaseStratifier
Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadDirection>
readDirectionStratifier
Stratifies bases into their read's Direction (i.e.static picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<String>
readgroupStratifier
Stratifies to the readgroup id of the read.static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadOrdinality>
readOrdinalityStratifier
Stratifies bases into their read's Ordinality (i.e.static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.PairOrientation>
readOrientationStratifier
Stratifies bases into their read-pair's Orientation (i.e.static ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ProperPaired>
readPairednessStratifier
Stratifies bases into their read's Proper-pairednessstatic ReadBaseStratification.RecordAndOffsetStratifier<Character>
referenceBaseStratifier
Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.static ReadBaseStratification.RecordAndOffsetStratifier<Integer>
softClipsLengthStratifier
Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.static ReadBaseStratification.RecordAndOffsetStratifier<String>
twoBasePaddedContextStratifier
Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
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Constructor Summary
Constructors Constructor Description ReadBaseStratification()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static htsjdk.samtools.CigarElement
getIndelElement(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset)
static <T extends Comparable<T>,S extends Comparable<S>>
ReadBaseStratification.PairStratifier<T,S>PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T> leftStratifier, ReadBaseStratification.RecordAndOffsetStratifier<S> rightStratifier, String suffix)
A factory for generating "pair" stratifier instances from two stratifiers and a stringstatic void
setGcCacheSize(int gcCacheSize)
static void
setLocationBinSize(int locationBinSize)
defaults to 2500static void
setLongHomopolymer(int longHomopolymer)
defaults to 6
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Field Detail
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currentReadBaseStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Character> currentReadBaseStratifier
Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e. complemented if needed)
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previousReadBaseStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Character> previousReadBaseStratifier
Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e. complemented if needed)
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nextReadBaseStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Character> nextReadBaseStratifier
Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e. complemented if needed)
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referenceBaseStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Character> referenceBaseStratifier
Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
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postDiNucleotideStratifier
public static final ReadBaseStratification.PairStratifier<Character,Character> postDiNucleotideStratifier
Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
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preDiNucleotideStratifier
public static final ReadBaseStratification.PairStratifier<Character,Character> preDiNucleotideStratifier
Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
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homoPolymerLengthStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Integer> homoPolymerLengthStratifier
Stratifies a base onto the length of the homopolymer preceding it (in the read direction). Read direction and only the preceding bases are taken into account (i.e. ignoring reference and current base).
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homopolymerStratifier
public static final ReadBaseStratification.PairStratifier<Integer,Pair<Character,Character>> homopolymerStratifier
Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came. Read direction and only the preceding bases are taken into account.
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binnedHomopolymerStratifier
public static final htsjdk.samtools.util.Lazy<ReadBaseStratification.PairStratifier<ReadBaseStratification.LongShortHomopolymer,Pair<Character,Character>>> binnedHomopolymerStratifier
Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came. Read direction and only the preceding bases are taken into account.This is done with a Lazy wrapper since it requires access to
LONG_HOMOPOLYMER
which can be set withsetLongHomopolymer(int)
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oneBasePaddedContextStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<String> oneBasePaddedContextStratifier
Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
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twoBasePaddedContextStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<String> twoBasePaddedContextStratifier
Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
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nonStratifier
public static final picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<String> nonStratifier
A constant stratifier which places all the reads into a single stratum.
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gcContentStratifier
public static final ReadBaseStratification.GCContentStratifier gcContentStratifier
A stratifier that uses GC (of the read) to stratify. Since the reads are expected to be seen over and over again, the GC is cachedStratification happens into (integer) percents.
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flowCellTileStratifier
public static final ReadBaseStratification.FlowCellTileStratifier flowCellTileStratifier
Stratifies base into their read's tile which is parsed from the read-name.
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flowCellXStratifier
public static final ReadBaseStratification.FlowCellXStratifier flowCellXStratifier
Stratifies base into their read's tile which is parsed from the read-name.
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flowCellYStratifier
public static final ReadBaseStratification.FlowCellYStratifier flowCellYStratifier
Stratifies base into their read's tile which is parsed from the read-name.
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readgroupStratifier
public static final picard.sam.SamErrorMetric.ReadBaseStratification.RecordStratifier<String> readgroupStratifier
Stratifies to the readgroup id of the read.
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readOrdinalityStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadOrdinality> readOrdinalityStratifier
Stratifies bases into their read's Ordinality (i.e. First or Second)
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readPairednessStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ProperPaired> readPairednessStratifier
Stratifies bases into their read's Proper-pairedness
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readDirectionStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.ReadDirection> readDirectionStratifier
Stratifies bases into their read's Direction (i.e. forward or reverse)
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readOrientationStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.PairOrientation> readOrientationStratifier
Stratifies bases into their read-pair's Orientation (i.e. F1R2, F2R1, F1F2 or R1R2)
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binnedReadCycleStratifier
public static final ReadBaseStratification.BinnedReadCycleStratifier binnedReadCycleStratifier
Stratifies into quintiles of read cycle.
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baseCycleStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Integer> baseCycleStratifier
Get the one-based cycle number of the base, taking the direction of the read into account
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insertLengthStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Integer> insertLengthStratifier
Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
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softClipsLengthStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Integer> softClipsLengthStratifier
Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
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baseQualityStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Byte> baseQualityStratifier
Stratifies into the base-quality of the base under consideration
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mappingQualityStratifier
public static final ReadBaseStratification.RecordAndOffsetStratifier<Integer> mappingQualityStratifier
Stratifies into the mapping-quality of the read under consideration
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mismatchesInReadStratifier
public static final ReadBaseStratification.MismatchesInReadStratifier mismatchesInReadStratifier
Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
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consensusStratifier
public static final ReadBaseStratification.ConsensusStratifier consensusStratifier
Stratify by tags used during duplex and single index consensus calling.
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nsInReadStratifier
public static final ReadBaseStratification.NsInReadStratifier nsInReadStratifier
Stratify by the number of Ns found in the read. This is particularly useful for data that has been consensus-called (a process that can add 'N' bases when there is no consensus)
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insertionsInReadStratifier
public static final ReadBaseStratification.CigarOperatorsInReadStratifier insertionsInReadStratifier
Stratify by Insertions in the read cigars.
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deletionsInReadStratifier
public static final ReadBaseStratification.CigarOperatorsInReadStratifier deletionsInReadStratifier
Stratify by Deletions in the read cigars.
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indelsInReadStratifier
public static final ReadBaseStratification.IndelsInReadStratifier indelsInReadStratifier
Stratify by Indels in the read cigars.
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indelLengthStratifier
public static final ReadBaseStratification.IndelLengthStratifier indelLengthStratifier
Stratifies into the number of bases in an insertion
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NOT_ALIGNED_ERROR
public static final int NOT_ALIGNED_ERROR
- See Also:
- Constant Field Values
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Method Detail
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setGcCacheSize
public static void setGcCacheSize(int gcCacheSize)
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setLongHomopolymer
public static void setLongHomopolymer(int longHomopolymer)
defaults to 6
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setLocationBinSize
public static void setLocationBinSize(int locationBinSize)
defaults to 2500
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PairStratifierFactory
public static <T extends Comparable<T>,S extends Comparable<S>> ReadBaseStratification.PairStratifier<T,S> PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T> leftStratifier, ReadBaseStratification.RecordAndOffsetStratifier<S> rightStratifier, String suffix)
A factory for generating "pair" stratifier instances from two stratifiers and a string- Type Parameters:
T
- the type of the left StratifierS
- the type of the right Stratifier- Parameters:
leftStratifier
- aReadBaseStratification.RecordAndOffsetStratifier
to userightStratifier
- aReadBaseStratification.RecordAndOffsetStratifier
to usesuffix
- the suffix to use for the new stratifier- Returns:
- an instance of
ReadBaseStratification.PairStratifier
that will stratify according to bothleftStratifier
andrightStratifier
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getIndelElement
public static htsjdk.samtools.CigarElement getIndelElement(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset)
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